#install.packages("pavo")
library("pavo")
Welcome to pavo 2! Take a look at the latest features (and update your bibliography) in our recent publication: Maia R., Gruson H., Endler J. A., White T. E. (2019) pavo 2: new tools for the spectral and spatial analysis of colour in R. Methods in Ecology and Evolution, 10, 1097-1107.
library("dplyr")
Attaching package: 㤼㸱dplyr㤼㸲
The following objects are masked from 㤼㸱package:stats㤼㸲:
filter, lag
The following objects are masked from 㤼㸱package:base㤼㸲:
intersect, setdiff, setequal, union
library("anchors")
Loading required package: rgenoud
## rgenoud (Version 5.8-3.0, Build Date: 2019-01-22)
## See http://sekhon.berkeley.edu/rgenoud for additional documentation.
## Please cite software as:
## Walter Mebane, Jr. and Jasjeet S. Sekhon. 2011.
## ``Genetic Optimization Using Derivatives: The rgenoud package for R.''
## Journal of Statistical Software, 42(11): 1-26.
##
Loading required package: MASS
Attaching package: 㤼㸱MASS㤼㸲
The following object is masked from 㤼㸱package:dplyr㤼㸲:
select
## anchors (Version 3.0-8, Build Date: 2014-02-24)
## See http://wand.stanford.edu/anchors for additional documentation and support.
library("ggplot2")
Keep up to date with changes at https://www.tidyverse.org/blog/
library("gridExtra")
Attaching package: 㤼㸱gridExtra㤼㸲
The following object is masked from 㤼㸱package:dplyr㤼㸲:
combine
getwd()
[1] "C:/Users/emmid/Desktop/Spec_Analysis"
Step 1: Organization and Processing
#create a data frame that includes frog IDs and path to directory with spec data
frog_dirs <- dir(path="SpecData", recursive=TRUE, include.dirs=TRUE, pattern= "(^\\d{1,}\\w{0,1}$)|(^..\\d$)")
spec_dirs<- file.path("SpecData", frog_dirs)
frog_IDs <- read.table(file.path("SpecData/Frog_IDs.txt"), header = TRUE, stringsAsFactors=FALSE)
spec_dirs_IDs <- mutate(frog_IDs, path=spec_dirs)
spec_dirs_IDs
#create a function to analyze and visualize spec data for each frog
dorsum_summary_total <- data.frame()
hindlimb_summary_total <- data.frame()
forelimb_summary_total <- data.frame()
for (y in c(1:91))
{
specs <- getspec(where=spec_dirs_IDs[y,2], ext='txt', lim=c(400,1041), subdir=TRUE, subdir.names=TRUE)
specs_graph <- explorespec(specs, ylim=c(0,50))
frog_ID <- spec_dirs_IDs[y,1]
#subset spec data for body region
#combine spec data within region and take the average
#apply LOESS smoothing, make neg values 0
#plot spectral curve
specs_dorsum <- na.omit(subset(specs, subset=c("a", "b", "c", "d", "e", "f", "p", "q")))
count_dorsum <- (ncol(specs_dorsum)-1)
dorsum_agg <- aggspec(specs_dorsum, by=count_dorsum, FUN="mean")
dorsum_agg_smooth <- procspec(dorsum_agg, opt="smooth", fixneg="zero", span=0.15)
dorsum_summary <- summary(dorsum_agg_smooth, subset = c("B2","S1Y", "S1R","H1"), wlmin=450, wlmax=950)
dorsum_summary$Individual_ID <- frog_ID
dorsum_summary_total <- rbind(dorsum_summary_total, dorsum_summary)
if (count_dorsum > 1)
{
dorsum_agg_plot <- aggplot(specs_dorsum, by=count_dorsum, ylim=c(0,50), xlim=c(450,950))
}
if (count_dorsum == 1)
{
dorsum_agg_plot <- plot(specs_dorsum, ylim=c(0,50), xlim=c(450,950))
}
specs_hindlimb <- na.omit(subset(specs, subset=c("g","h")))
count_hindlimb <- (ncol(specs_hindlimb)-1)
if (count_hindlimb == 2)
{
hindlimb_agg_plot <- aggplot(specs_hindlimb, by=count_hindlimb, ylim=c(0,50), xlim=c(450,950))
specs_hindlimb <- aggspec(specs_hindlimb, by=2, FUN="mean")
}
if (count_hindlimb == 2 || count_hindlimb == 1)
{
hindlimb_agg_smooth <- procspec(specs_hindlimb, opt="smooth", fixneg="zero", span=0.15)
hindlimb_summary <- summary(hindlimb_agg_smooth, subset = c("B2", "S1G", "S1R","H1"), wlmin=450, wlmax=950)
hindlimb_summary$Individual_ID <- frog_ID
hindlimb_summary_total <- rbind(hindlimb_summary_total, hindlimb_summary)
}
if (count_hindlimb == 1)
{
hindlimb_plot <- plot(specs_hindlimb, ylim=c(0,50), xlim=c(450,950))
}
specs_forelimb <- na.omit(subset(specs, subset=c("n", "o")))
count_forelimb <- (ncol(specs_forelimb)-1)
if (count_forelimb == 2)
{
forelimb_agg_plot <- aggplot(specs_forelimb, by=count_forelimb, ylim=c(0,50), xlim=c(450,950))
specs_forelimb <- aggspec(specs_forelimb, by=2, FUN="mean")
}
if (count_forelimb == 2 || count_forelimb == 1)
{
forelimb_agg_smooth <- procspec(specs_forelimb, opt="smooth", fixneg="zero", span=0.15)
forelimb_summary <- summary(forelimb_agg_smooth, subset = c("B2", "S1G", "S1R","H1"), wlmin=450, wlmax=950)
forelimb_summary$Individual_ID <- frog_ID
forelimb_summary_total <- rbind(forelimb_summary_total, forelimb_summary)
}
if (count_forelimb == 1)
{
forelimb_plot <- plot(specs_forelimb, ylim=c(0,50), xlim=c(450,950))
}
}
15 files found; importing spectra:
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm14 files found; importing spectra:
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm14 files found; importing spectra:
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
|
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|
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
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|
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
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|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
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|
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
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|
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
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|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
|
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|=================================================================================== | 93%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
|
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|
|=================================================================================== | 93%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
|
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|
|=================================================================================== | 93%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
|
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|============================================================================= | 87%
|
|=================================================================================== | 93%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
|
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|
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|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
|
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|============================================================================= | 87%
|
|=================================================================================== | 93%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
|
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|
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|============================================================================= | 87%
|
|=================================================================================== | 93%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
|
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|
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|
|============================================================================= | 87%
|
|=================================================================================== | 93%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
|
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|
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|============================================================================= | 87%
|
|=================================================================================== | 93%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
|
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|
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|============================================================================= | 87%
|
|=================================================================================== | 93%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
|
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|============================================================================= | 87%
|
|=================================================================================== | 93%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
|
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|============================================================================= | 87%
|
|=================================================================================== | 93%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
|
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|
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|============================================================================= | 87%
|
|=================================================================================== | 93%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
|
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|================================================================= | 73%
|
|======================================================================= | 80%
|
|============================================================================= | 87%
|
|=================================================================================== | 93%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
|
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|
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|
|================================================================= | 73%
|
|======================================================================= | 80%
|
|============================================================================= | 87%
|
|=================================================================================== | 93%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
|
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|
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|
|================================================================= | 73%
|
|======================================================================= | 80%
|
|============================================================================= | 87%
|
|=================================================================================== | 93%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm5 files found; importing spectra:
|
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|
|================== | 20%
|
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|
|===================================================== | 60%
|
|======================================================================= | 80%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
Subset condition not found15 files found; importing spectra:
|
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|
|================================================================= | 73%
|
|======================================================================= | 80%
|
|============================================================================= | 87%
|
|=================================================================================== | 93%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
|
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|=========================================================== | 67%
|
|================================================================= | 73%
|
|======================================================================= | 80%
|
|============================================================================= | 87%
|
|=================================================================================== | 93%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
|
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|
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|
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|
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|
|=========================================================== | 67%
|
|================================================================= | 73%
|
|======================================================================= | 80%
|
|============================================================================= | 87%
|
|=================================================================================== | 93%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
|
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|
|============ | 13%
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
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|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
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|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
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|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm12 files found; importing spectra:
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
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|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
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|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm10 files found; importing spectra:
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|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
8 files found; importing spectra:
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|
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
Subset condition not found12 files found; importing spectra:
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|
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|
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm6 files found; importing spectra:
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
Subset condition not found15 files found; importing spectra:
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|============================================================================= | 87%
|
|=================================================================================== | 93%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm7 files found; importing spectra:
|
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|============= | 14%
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|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
Subset condition not found8 files found; importing spectra:
|
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|=========== | 12%
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|============================================================================== | 88%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
Subset condition not found7 files found; importing spectra:
|
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|============= | 14%
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|====================================== | 43%
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|
|================================================================ | 71%
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|============================================================================ | 86%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
11 files found; importing spectra:
|
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|======== | 9%
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|======================== | 27%
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|
|========================================================================= | 82%
|
|================================================================================= | 91%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm6 files found; importing spectra:
|
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|
|=============== | 17%
|
|============================== | 33%
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|============================================ | 50%
|
|=========================================================== | 67%
|
|========================================================================== | 83%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nmprocessing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
7 files found; importing spectra:
|
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|
|============= | 14%
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|=================================================== | 57%
|
|================================================================ | 71%
|
|============================================================================ | 86%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm8 files found; importing spectra:
|
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|
|=========== | 12%
|
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|================================= | 38%
|
|============================================ | 50%
|
|======================================================== | 62%
|
|=================================================================== | 75%
|
|============================================================================== | 88%
|
|=========================================================================================| 100%
Subset condition not foundprocessing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
7 files found; importing spectra:
|
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|
|============= | 14%
|
|========================= | 29%
|
|====================================== | 43%
|
|=================================================== | 57%
|
|================================================================ | 71%
|
|============================================================================ | 86%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
15 files found; importing spectra:
|
| | 0%
|
|====== | 7%
|
|============ | 13%
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|================== | 20%
|
|======================== | 27%
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|===================================================== | 60%
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|=========================================================== | 67%
|
|================================================================= | 73%
|
|======================================================================= | 80%
|
|============================================================================= | 87%
|
|=================================================================================== | 93%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm14 files found; importing spectra:
|
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|====== | 7%
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|
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|
|============================================================================ | 86%
|
|=================================================================================== | 93%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm10 files found; importing spectra:
|
| | 0%
|
|========= | 10%
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|
|======================================================================= | 80%
|
|================================================================================ | 90%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nmSubset condition not found5 files found; importing spectra:
|
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|
|================== | 20%
|
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|
|===================================================== | 60%
|
|======================================================================= | 80%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
Subset condition not found5 files found; importing spectra:
|
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|
|================== | 20%
|
|==================================== | 40%
|
|===================================================== | 60%
|
|======================================================================= | 80%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
Subset condition not found8 files found; importing spectra:
|
| | 0%
|
|=========== | 12%
|
|====================== | 25%
|
|================================= | 38%
|
|============================================ | 50%
|
|======================================================== | 62%
|
|=================================================================== | 75%
|
|============================================================================== | 88%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm9 files found; importing spectra:
|
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|
|========== | 11%
|
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|
|===================================================================== | 78%
|
|=============================================================================== | 89%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm7 files found; importing spectra:
|
| | 0%
|
|============= | 14%
|
|========================= | 29%
|
|====================================== | 43%
|
|=================================================== | 57%
|
|================================================================ | 71%
|
|============================================================================ | 86%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nmSubset condition not found15 files found; importing spectra:
|
| | 0%
|
|====== | 7%
|
|============ | 13%
|
|================== | 20%
|
|======================== | 27%
|
|============================== | 33%
|
|==================================== | 40%
|
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|
|=============================================== | 53%
|
|===================================================== | 60%
|
|=========================================================== | 67%
|
|================================================================= | 73%
|
|======================================================================= | 80%
|
|============================================================================= | 87%
|
|=================================================================================== | 93%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm6 files found; importing spectra:
|
| | 0%
|
|=============== | 17%
|
|============================== | 33%
|
|============================================ | 50%
|
|=========================================================== | 67%
|
|========================================================================== | 83%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
Subset condition not found3 files found; importing spectra:
|
| | 0%
|
|============================== | 33%
|
|=========================================================== | 67%
|
|=========================================================================================| 100%
Subset condition not foundprocessing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
10 files found; importing spectra:
|
| | 0%
|
|========= | 10%
|
|================== | 20%
|
|=========================== | 30%
|
|==================================== | 40%
|
|============================================ | 50%
|
|===================================================== | 60%
|
|============================================================== | 70%
|
|======================================================================= | 80%
|
|================================================================================ | 90%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nmprocessing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
8 files found; importing spectra:
|
| | 0%
|
|=========== | 12%
|
|====================== | 25%
|
|================================= | 38%
|
|============================================ | 50%
|
|======================================================== | 62%
|
|=================================================================== | 75%
|
|============================================================================== | 88%
|
|=========================================================================================| 100%
Subset condition not foundSubset condition not found6 files found; importing spectra:
|
| | 0%
|
|=============== | 17%
|
|============================== | 33%
|
|============================================ | 50%
|
|=========================================================== | 67%
|
|========================================================================== | 83%
|
|=========================================================================================| 100%
Subset condition not foundSubset condition not found3 files found; importing spectra:
|
| | 0%
|
|============================== | 33%
|
|=========================================================== | 67%
|
|=========================================================================================| 100%
Subset condition not foundSubset condition not found9 files found; importing spectra:
|
| | 0%
|
|========== | 11%
|
|==================== | 22%
|
|============================== | 33%
|
|======================================== | 44%
|
|================================================= | 56%
|
|=========================================================== | 67%
|
|===================================================================== | 78%
|
|=============================================================================== | 89%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
8 files found; importing spectra:
|
| | 0%
|
|=========== | 12%
|
|====================== | 25%
|
|================================= | 38%
|
|============================================ | 50%
|
|======================================================== | 62%
|
|=================================================================== | 75%
|
|============================================================================== | 88%
|
|=========================================================================================| 100%
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
Subset condition not found10 files found; importing spectra:
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm5 files found; importing spectra:
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processing options applied:
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Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nmSubset condition not found15 files found; importing spectra:
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm15 files found; importing spectra:
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processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
processing options applied:
smoothing spectra with a span of 0.15
Negative value correction: converted negative values to zero
cannot calculate blue chroma; wavelength range not between 400 and 510 nmcannot calculate UV chroma; wavelength range not below 400 nmcannot calculate violet chroma; wavelength below 415 nm
dorsum_summary_total
hindlimb_summary_total
forelimb_summary_total
write.table(dorsum_summary_total, file="Spec_Results/dorsum_summary.txt", sep="\t", row.names = FALSE, na="x", col.names = TRUE, quote=FALSE)
write.table(hindlimb_summary_total, file="Spec_Results/hindlimb_summary.txt", sep="\t", row.names = FALSE, na="x", col.names = TRUE, quote=FALSE)
individual_key <- read.csv("SpecData/Individual_Key.csv")
individual_key
pedigree_info <- read.csv("pedigree_info_new.csv", colClasses = "character")
pedigree_info <- transform(pedigree_info, rotation_score = as.numeric(rotation_score))
pedigree_info
ped_dorsum <- merge(pedigree_info, dorsum_summary_total, by.y="Individual_ID", no.dups=TRUE, all.x=TRUE)
ped_dorsum <- ped_dorsum[,c(2,1,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18)]
ped_dorsum
ped_forelimb <- merge(pedigree_info, forelimb_summary_total, by.y="Individual_ID", no.dups=TRUE, all.x=TRUE)
ped_forelimb <- ped_forelimb[,c(2,1,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18)]
ped_forelimb
ped_hindlimb <- merge(pedigree_info, hindlimb_summary_total, by.y="Individual_ID", no.dups=TRUE, all.x=TRUE)
ped_hindlimb <- ped_hindlimb[,c(2,1,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18)]
ped_hindlimb
Find average phenotypes for purebred individuals and input those values for purebred individuals with missing phenotypes
Hu_dorsum <- ped_dorsum[1:3,(15:18)]
Hu_dorsum_means <- as.data.frame(colMeans(Hu_dorsum, na.rm=TRUE))
ped_dorsum[3,15:18]=Hu_dorsum_means[1:4,1]
ped_dorsum
Hu_forelimb <- ped_forelimb[1:3,(15:18)]
Hu_forelimb_means <- as.data.frame(colMeans(Hu_forelimb, na.rm=TRUE))
ped_forelimb[3,15:18]=Hu_forelimb_means[1:4,1]
ped_forelimb
Hu_hindlimb <- ped_hindlimb[1:3,(15:18)]
Hu_hindlimb_means <- as.data.frame(colMeans(Hu_hindlimb, na.rm=TRUE))
ped_hindlimb[3,15:18]=Hu_hindlimb_means[1:4,1]
ped_hindlimb
Sa_dorsum <- ped_dorsum[c(4,22,70),(14:18)]
Sa_dorsum_means <- as.data.frame(colMeans(Sa_dorsum, na.rm=TRUE))
ped_dorsum[70,14:18]=Sa_dorsum_means[1:5,1]
ped_dorsum
Sa_forelimb <- ped_forelimb[c(4,22,70),(14:18)]
Sa_forelimb_means <- as.data.frame(colMeans(Sa_forelimb, na.rm=TRUE))
ped_forelimb[70,14:18]=Sa_forelimb_means[1:5,1]
ped_forelimb
Sa_hindlimb <- ped_hindlimb[c(4,22,70),(14:18)]
Sa_hindlimb_means <- as.data.frame(colMeans(Sa_hindlimb, na.rm=TRUE))
ped_hindlimb[70,14:18]=Sa_hindlimb_means[1:5,1]
ped_hindlimb
NA
write.table(ped_dorsum, file="Spec_Results/Ped_Files/ped_dorsum.txt", sep="\t", row.names = FALSE, na="", col.names = TRUE, quote=FALSE)
write.table(ped_forelimb, file="Spec_Results/Ped_Files/ped_forelimb.txt", sep="\t", row.names = FALSE, na="", col.names = TRUE, quote=FALSE)
write.table(ped_hindlimb, file="Spec_Results/Ped_Files/ped_hindlimb.txt", sep="\t", row.names = FALSE, na="", col.names = TRUE, quote=FALSE)
Change IDs to numbers for easier Merlin analysis
ped_dorsum_nums <- ped_dorsum
for (y in c(1:88))
{ped_dorsum_nums <- replace.value(ped_dorsum_nums, c("Individual_ID", "Parent_1", "Parent_2"), from=individual_key[y,1], to=individual_key[y,2])}
ped_forelimb_nums <- ped_forelimb
for (y in c(1:88))
{ped_forelimb_nums <- replace.value(ped_forelimb_nums, c("Individual_ID", "Parent_1", "Parent_2"), from=individual_key[y,1], to=individual_key[y,2])}
ped_hindlimb_nums <- ped_hindlimb
for (y in c(1:88))
{ped_hindlimb_nums <- replace.value(ped_hindlimb_nums, c("Individual_ID", "Parent_1", "Parent_2"), from=individual_key[y,1], to=individual_key[y,2])}
write.table(ped_dorsum_nums, file="Spec_Results/Ped_Files/ped_dorsum_all.txt", sep="\t", row.names = FALSE, na="x", col.names = FALSE, quote=FALSE)
write.table(ped_forelimb_nums, file="Spec_Results/Ped_Files/ped_forelimb_all.txt", sep="\t", row.names = FALSE, na="x", col.names = FALSE, quote=FALSE)
write.table(ped_hindlimb_nums, file="Spec_Results/Ped_Files/ped_hindlimb_all.txt", sep="\t", row.names = FALSE, na="x", col.names = FALSE, quote=FALSE)
Separate ASIP ped file and save
ped_dorsum_asip <- subset(ped_dorsum_nums, select=c(Fam:asip2, rotation_score:H1))
ped_dorsum_asip
ped_forelimb_asip <- subset(ped_forelimb_nums, select=c(Fam:asip2, B2:H1))
ped_forelimb_asip
ped_hindlimb_asip <- subset(ped_hindlimb_nums, select=c(Fam:asip2, B2:H1))
ped_hindlimb_asip
write.table(ped_dorsum_asip, file="Spec_Results/Ped_Files/ped_dorsum_asip.txt", sep="\t", row.names = FALSE, na="x", col.names = FALSE, quote=FALSE)
write.table(ped_forelimb_asip, file="Spec_Results/Ped_Files/ped_forelimb_asip.txt", sep="\t", row.names = FALSE, na="x", col.names = FALSE, quote=FALSE)
write.table(ped_hindlimb_asip, file="Spec_Results/Ped_Files/ped_hindlimb_asip.txt", sep="\t", row.names = FALSE, na="x", col.names = FALSE, quote=FALSE)
Separate mc1r ped file and save
ped_dorsum_mc1r <- subset(ped_dorsum_nums, select= c(Fam:Sex,mc1r1:mc1r2, rotation_score:H1))
ped_dorsum_mc1r
ped_forelimb_mc1r <- subset(ped_forelimb_nums,select= c(Fam:Sex,mc1r1:mc1r2, B2:H1))
ped_forelimb_mc1r
ped_hindlimb_mc1r <- subset(ped_hindlimb_nums,select= c(Fam:Sex,mc1r1:mc1r2, B2:H1))
ped_hindlimb_mc1r
write.table(ped_dorsum_mc1r, file="Spec_Results/Ped_Files/ped_dorsum_mc1r.txt", sep="\t", row.names = FALSE, na="x", col.names = FALSE, quote=FALSE)
write.table(ped_forelimb_mc1r, file="Spec_Results/Ped_Files/ped_forelimb_mc1r.txt", sep="\t", row.names = FALSE, na="x", col.names = FALSE, quote=FALSE)
write.table(ped_hindlimb_mc1r, file="Spec_Results/Ped_Files/ped_hindlimb_mc1r.txt", sep="\t", row.names = FALSE, na="x", col.names = FALSE, quote=FALSE)
Separate bsn2 ped file and save
ped_dorsum_bsn2 <- subset(ped_dorsum_nums, select= c(Fam:Sex,bsn2.1:bsn2.2, rotation_score:H1))
ped_dorsum_bsn2
ped_forelimb_bsn2 <- subset(ped_forelimb_nums,select= c(Fam:Sex,bsn2.1:bsn2.2, B2:H1))
ped_forelimb_bsn2
ped_hindlimb_bsn2 <- subset(ped_hindlimb_nums,select= c(Fam:Sex,bsn2.1:bsn2.2, B2:H1))
ped_hindlimb_bsn2
write.table(ped_dorsum_bsn2, file="Spec_Results/Ped_Files/ped_dorsum_bsn2.txt", sep="\t", row.names = FALSE, na="x", col.names = FALSE, quote=FALSE)
write.table(ped_forelimb_bsn2, file="Spec_Results/Ped_Files/ped_forelimb_bsn2.txt", sep="\t", row.names = FALSE, na="x", col.names = FALSE, quote=FALSE)
write.table(ped_hindlimb_bsn2, file="Spec_Results/Ped_Files/ped_hindlimb_bsn2.txt", sep="\t", row.names = FALSE, na="x", col.names = FALSE, quote=FALSE)
separate retsat ped file and save
ped_dorsum_retsat <- subset(ped_dorsum_nums, select= c(Fam:Sex,retsat1:retsat2, rotation_score:H1))
ped_dorsum_retsat
ped_forelimb_retsat <- subset(ped_forelimb_nums, select= c(Fam:Sex,retsat1:retsat2, B2:H1))
ped_forelimb_retsat
ped_hindlimb_retsat <- subset(ped_hindlimb_nums, select= c(Fam:Sex,retsat1:retsat2, B2:H1))
ped_hindlimb_retsat
write.table(ped_dorsum_retsat, file="Spec_Results/Ped_Files/ped_dorsum_retsat.txt", sep="\t", row.names = FALSE, na="x", col.names = FALSE, quote=FALSE)
write.table(ped_forelimb_retsat, file="Spec_Results/Ped_Files/ped_forelimb_retsat.txt", sep="\t", row.names = FALSE, na="x", col.names = FALSE, quote=FALSE)
write.table(ped_hindlimb_retsat, file="Spec_Results/Ped_Files/ped_hindlimb_retsat.txt", sep="\t", row.names = FALSE, na="x", col.names = FALSE, quote=FALSE)
ped_dorsum_asip$genotype <- paste(ped_dorsum_asip$asip1,ped_dorsum_asip$asip2)
ped_dorsum_asip_new <- ped_dorsum_asip[ped_dorsum_asip$genotype!="x x",]
asip_rot <- ggplot(data=ped_dorsum_asip_new) + geom_boxplot(mapping=aes(x=genotype, y=rotation_score)) + ggtitle("Asip: Rotation")
ped_dorsum_asip$genotype <- paste(ped_dorsum_asip$asip1,ped_dorsum_asip$asip2)
ped_dorsum_asip_new <- ped_dorsum_asip[ped_dorsum_asip$genotype!="x x",]
asip_B2 <- ggplot(data=ped_dorsum_asip_new) + geom_boxplot(mapping=aes(x=genotype, y=B2)) + ggtitle("Asip: Dorsal B2")
ped_dorsum_asip$genotype <- paste(ped_dorsum_asip$asip1,ped_dorsum_asip$asip2)
ped_dorsum_asip_new <- ped_dorsum_asip[ped_dorsum_asip$genotype!="x x",]
asip_S1R <- ggplot(data=ped_dorsum_asip_new) + geom_boxplot(mapping=aes(x=genotype, y=S1R)) + ggtitle("Asip: Dorsal S1R")
#png(file="C:/Users/emmid/Desktop/Research/Figures/asip_tables.png")
grid.arrange(asip_rot, asip_B2, asip_S1R, nrow=2)
#dev.off()
ped_dorsum_bsn2$genotype <- paste(ped_dorsum_bsn2$bsn2.1,ped_dorsum_bsn2$bsn2.2)
ped_dorsum_bsn2_new <- ped_dorsum_bsn2[ped_dorsum_bsn2$genotype!="x x",]
bsn2_rot <- ggplot(data=ped_dorsum_bsn2_new) + geom_boxplot(mapping=aes(x=genotype, y=rotation_score)) + ggtitle("Bsn: Rotation")
ped_hindlimb_bsn2$genotype <- paste(ped_dorsum_bsn2$bsn2.1,ped_hindlimb_bsn2$bsn2.2)
ped_hindlimb_bsn2_new <- ped_hindlimb_bsn2[ped_hindlimb_bsn2$genotype!="x x",]
bsn2_S1G <- ggplot(data=ped_hindlimb_bsn2_new) + geom_boxplot(mapping=aes(x=genotype, y=S1G)) + ggtitle("Bsn: Hindlimb S1G")
#png(file="C:/Users/emmid/Desktop/Research/Figures/bsn2_tables.png")
grid.arrange(bsn2_rot, bsn2_S1G, ncol=2, widths=c(10,10), heights=c(10,10))
#dev.off()
ped_dorsum_mc1r$genotype <- paste(ped_dorsum_mc1r$mc1r1,ped_dorsum_mc1r$mc1r2)
ped_dorsum_mc1r_new <- ped_dorsum_mc1r[ped_dorsum_mc1r$genotype!="x x",]
mc1r_rot <- ggplot(data=ped_dorsum_mc1r_new) + geom_boxplot(mapping=aes(x=genotype, y=rotation_score)) + ggtitle("Mc1r: Rotation")
ped_hindlimb_mc1r$genotype <- paste(ped_hindlimb_mc1r$mc1r1,ped_hindlimb_mc1r$mc1r2)
ped_hindlimb_mc1r_new <- ped_hindlimb_mc1r[ped_hindlimb_mc1r$genotype!="x x",]
mc1r_B2 <- ggplot(data=ped_hindlimb_mc1r_new) + geom_boxplot(mapping=aes(x=genotype, y=B2)) + ggtitle("Mc1r: Hindlimb B2")
ped_hindlimb_mc1r$genotype <- paste(ped_hindlimb_mc1r$mc1r1,ped_hindlimb_mc1r$mc1r2)
ped_hindlimb_mc1r_new <- ped_hindlimb_mc1r[ped_hindlimb_mc1r$genotype!="x x",]
mc1r_S1R <- ggplot(data=ped_hindlimb_mc1r_new) + geom_boxplot(mapping=aes(x=genotype, y=S1R)) + ggtitle("Mc1r: Hindlimb S1R")
ped_hindlimb_mc1r$genotype <- paste(ped_hindlimb_mc1r$mc1r1,ped_hindlimb_mc1r$mc1r2)
ped_hindlimb_mc1r_new <- ped_hindlimb_mc1r[ped_hindlimb_mc1r$genotype!="x x",]
mc1r_H1 <- ggplot(data=ped_hindlimb_mc1r_new) + geom_boxplot(mapping=aes(x=genotype, y=H1)) + ggtitle("Mc1r: Hindlimb Hue")
#png(file="C:/Users/emmid/Desktop/Research/Figures/mc1r_tables.png")
grid.arrange(mc1r_rot, mc1r_B2, mc1r_S1R, nrow=2)
#dev.off()
ped_dorsum_retsat$genotype <- paste(ped_dorsum_retsat$retsat1,ped_dorsum_retsat$retsat2)
ped_dorsum_retsat_new <- ped_dorsum_retsat[ped_dorsum_retsat$genotype!="x x",]
retsat_rot <- ggplot(data=ped_dorsum_retsat_new) + geom_boxplot(mapping=aes(x=genotype, y=rotation_score)) + ggtitle("Retsat: Rotation")
ped_dorsum_retsat$genotype <- paste(ped_dorsum_retsat$retsat1,ped_dorsum_retsat$retsat2)
ped_dorsum_retsat_new <- ped_dorsum_retsat[ped_dorsum_retsat$genotype!="x x",]
retsat_S1Y <- ggplot(data=ped_dorsum_retsat_new) + geom_boxplot(mapping=aes(x=genotype, y=S1Y)) + ggtitle("Retsat: Dorsal S1Y")
ped_dorsum_retsat$genotype <- paste(ped_dorsum_retsat$retsat1,ped_dorsum_retsat$retsat2)
ped_dorsum_retsat_new <- ped_dorsum_retsat[ped_dorsum_retsat$genotype!="x x",]
retsat_S1R <- ggplot(data=ped_dorsum_retsat_new) + geom_boxplot(mapping=aes(x=genotype, y=S1R)) + ggtitle("Retsat: Dorsal Red")
ped_dorsum_retsat$genotype <- paste(ped_dorsum_retsat$retsat1,ped_dorsum_retsat$retsat2)
ped_dorsum_retsat_new <- ped_dorsum_retsat[ped_dorsum_retsat$genotype!="x x",]
retsat_H1 <- ggplot(data=ped_dorsum_retsat_new) + geom_boxplot(mapping=aes(x=genotype, y=H1)) + ggtitle("Retsat: Dorsal Hue")
#png(file="C:/Users/emmid/Desktop/Research/Figures/retsat_tables.png")
grid.arrange(retsat_rot, retsat_S1Y, retsat_H1, nrow=2)
#dev.off()
png(file="C:/Users/emmid/Desktop/Research/Figures/boxplots.png")
grid.arrange(asip_rot,asip_B2,bsn2_rot,mc1r_rot,mc1r_B2,retsat_rot,retsat_S1Y, ncol=3, widths=c(15,15,15))
dev.off()
null device
1
asip_B2_new <- ggplot(data=ped_dorsum_asip_new) + geom_boxplot(mapping=aes(x=genotype, y=B2))+xlab("Asip genotype")+ylab("Dorsal Coloration")+theme(text= element_text(size=20))
asip_B2_new
mc1r_rot_new <- ggplot(data=ped_dorsum_mc1r_new) + geom_boxplot(mapping=aes(x=genotype, y=rotation_score))+xlab("Mc1r genotype")+ylab("Dorsal Pattern")+theme(text= element_text(size=20))
mc1r_rot_new
png(file="C:/Users/emmid/Desktop/Research/Figures/asip_boxplot.png")
asip_B2_new
dev.off()
png
2
png(file="C:/Users/emmid/Desktop/Research/Figures/mc1r_boxplot.png")
mc1r_rot_new
dev.off()
png
2